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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
eastgenomics/mini_uranus_just_bwamem Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
//input = null
reads = null
bwa_index = null
// MOSDEPTH
mosdepth_bed = null
mosdepth_window_size = 500
//mosdepth_fast_mode = false
outdir = 'results'
// CGPPINDEL
docker.enabled = true
cgppindel_id = "cb44a611a143"
help = false
seqtype = 'TG'
tumour = '/home/raymondmiles/Desktop/software_engineering_module/cgppindel_local/tumour_bamfile_markdup.bam'
tumour_index = '/home/raymondmiles/Desktop/Software_Development/cgppindel_bashexperiment/subset.bam.bai' \
normal = '/home/raymondmiles/Desktop/software_engineering_module/cgppindel_local/TA2_S59_L008_tumor_markdup.bam'
normal_index = '/home/raymondmiles/Desktop/Software_Development/software_module_master/eastgenomics-mini_uranus/TA2_S59_L008_tumor_markdup_nochr.bam.bai' \
genomefa = '/home/raymondmiles/Desktop/Software_Development/software_module_master/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18_noChr.fasta'
genes = '/home/raymondmiles/Desktop/software_engineering_module/cgppindel_local/coding_unrestricted_GRCh38_myeloid_v1.0.bed'
unmatched = '/home/raymondmiles/Desktop/software_engineering_module/cgppindel_local/normalPanel.gff3.gz'
simrep = '/home/raymondmiles/Desktop/software_engineering_module/cgppindel_local/simpleRepeats_sorted.bed.gz'
simrep_index = '/home/raymondmiles/Desktop/Software_Development/software_module_master/eastgenomics-mini_uranus/simpleRepeats_sorted_withoutchr.bed.gz.tbi'
filter = '/home/raymondmiles/Desktop/software_engineering_module/cgppindel_local/targetedRulemks.lst'
assembly = 'GRCh38'
species = "Human"
genomefa_fai = "/home/raymondmiles/Desktop/Software_Development/software_module_master/eastgenomics-mini_uranus/GRCh38.no_alt_analysis_set_chr_mask21.fa.fai"
project_dir = '/home/raymondmiles/Desktop/Software_Development/software_module_master/eastgenomics-mini_uranus/'
docker_image = "/home/raymondmiles/Desktop/Software_Development/cgppindel_bashexperiment/cgppindel_image.tar"
// Boilerplate options
//outdir = null
publish_dir_mode = 'copy'
monochrome_logs = false
version = false
}
/// bwa mem ///
process {
resourceLimits = [
cpus: 5
]
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
//container = 'quay.io/wtsicgp/cgppindel:3.9.0'
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
//docker.runOptions = '-u $(id -u):$(id -g) -v /home/raymondmiles/Desktop/Software_Development/software_module_master/eastgenomics-mini_uranus:/data'
docker.runOptions = '-u $(id -u):$(id -g)'
process {
memory = 9.GB // Default memory limit for all processes when using Docker
cpus = 6
}
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
laptop {
process {
cpus = 5
withLabel:process_high {
memory = 12.GB // need to set an appropriate limit
cpus = 5
}
withName: 'SAMTOOLS_SORT' {
memory = 8.GB // Limit total memory to 15GB
//ext.args = '-m 2G' // Limit memory per thread to 2GB
cpus = 5 // Limit the number of threads (adjust as needed)
}
withName: 'SAMTOOLS_INDEX' {
memory = 8.GB // Limit total memory to 15GB
cache = false
//ext.args = '-m 2G' // Limit memory per thread to 2GB
cpus = 6 // Limit the number of threads (adjust as needed)
}
withName: 'MOSDEPTH' {
memory = 8.GB // Limit total memory to 15GB
//ext.args = '-m 2G' // Limit memory per thread to 2GB
cpus = 6 // Limit the number of threads (adjust as needed)
}
withName: 'BWA_MEM' {
memory = 8.GB // Limit total memory to 15GB
//ext.args = "-R '@RG\\tID:134866926-25014Q0045-25NGSHO3-8128-U-96527893_S48_L001_001_1\\tPL:ILLUMINA\\tPU:134866926-25014Q0045-25NGSHO3-8128-U-96527893_S48_L001_001_1\\tLB:134866926-25014Q0045-25NGSHO3-8128-U-96527893\\tSM:134866926-25014Q0045-25NGSHO3-8128-U-96527893'"
ext.args = {"-R '@RG\\tID:$meta.id\\tPL:ILLUMINA\\tPU:$meta.id\\tLB:$meta.id\\tSM:$meta.id'"}
//ext.args = '-m 2G' // Limit memory per thread to 2GB
cpus = 6 // Limit the number of threads (adjust as needed)
}
withName: 'EXTRACT_BWA_INDEX' {
memory = 8.GB // Limit total memory to 15GB
//ext.args = '-m 2G' // Limit memory per thread to 2GB
//ext.args2 = '-R @RG\tID:134866926-25014Q0045-25NGSHO3-8128-U-96527893_S48_L001_001_1\tPL:ILLUMINA\tPU:134866926-25014Q0045-25NGSHO3-8128-U-96527893_S48_L001_001_1\tLB:134866926-25014Q0045-25NGSHO3-8128-U-96527893\tSM:134866926-25014Q0045-25NGSHO3-8128-U-96527893'
cpus = 6 // Limit the number of threads (adjust as needed)
}
}
docker.enabled = true // or singularity.enabled = true if you prefer Singularity
}
}
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'eastgenomics/mini_uranus_just_bwamem'
author = """RCM"""
homePage = 'https://github.com/eastgenomics/mini_uranus_just_bwamem'
description = """justsinglebwamem"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '1.0.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'